Currently, there are abilities to take notes on the Bible, and maybe commentaries, by using the user notes feature. However, currently, there is not a real good way to take notes on any tools without having a separate user tool, word doc, or old-fashioned pen and paper. And these are not tied to the tool like user notes are tied to verses.

I am the type that likes to take notes on various things (margin notes, etc). It would be fantastic if there was the ability to take notes right on any tools (obviously that would be stored as an external file), but that I would see whenever I look at that tool... even if it was something like a "sticky note" feature.